Exploring alternative patterns of descent
Re-assigning the primary founder
There may be cases where you believe that the primary founder
predicted by eBURST is wrong, or where there are two possible
founders with substantial bootstrap support and you would
like to explore how the eBURST diagram would look if the
alternative ST was assigned as the primary founder.
to re-assign the primary founder (see
here for details
of how to do this) can change the diagram substantially
as many STs may be SLVs of both the predicted primary founder
and an alternative plausible primary founder, but are preferentially
assigned to the primary founder (the true number of SLVs
of any ST are shown in the Analysis Window).
Re-assigning the primary founder will now preferentially
assign all of these SLVs to the user-selected primary founder.
Figure 3 shows an example of an eBURST
diagram shown with the primary founder assigned by eBURST
(blue) and re-drawn
with a user-defined ST as the primary founder (red).
The diagrams represent the unedited output of eBURST v2.
example, the lineage 3 clonal complex of N. meningitidis,
we proposed in Feil et al. (2004) that ST303 (arrow)
may have been the near extinct founding ST of this large
complex, although it is not assigned as the primary founder
by eBURST. To explore this further, the diagram is re-drawn
with ST303 as the user-defined primary founder, which
shows that ST303 has many SLVs and looks a plausible founder.
This is also supported by the fact that ST303 has the minimum
distance to all other STs in the clonal complex.
An illustrative example is shown in Figure 2. The initial
procedure identifies ST1 as the ST with the greatest number
of SLVs (the primary founder) and links ST1 to its seven
SLVs. It then assigns the SLVs of each of these seven SLVs,
and identifies ST2 as a SLV of ST17 and links it. Progressing
further outwards, the four descendent SLVs of ST2 are identified
and linked, and the process continues outwards and links
the four descendent SLVs of ST3. This initial assignment
of SLVs from the primary founder outwards results in STs
that are SLVs of more than one ST being preferentially
assigned to the more centrally positioned ST (ST2 in Figure
In the example shown in Figure 2, optimisation
identifies ST10 and ST12 as SLVs of ST3 as well as of ST2.
The optimisation procedure re-assigns STs to maximise the
numbers of SLVs associated with ST3 as this subgroup founder
has more SLVs than ST2 and thus is a more likely subgroup
founder. ST2 and ST3 each start with four SLVs and after
optimisation ST3 ends up with six linked SLVs (STs 10, 12,
13, 14, 15 and 16) and ST2 with two linked SLVs (STs 3 and
11). Optimisation re-organises the arrangement of STs to
maximise the numbers of SLVs associated with subgroup founders,
closely approximating the sub-groups produced by the original
BURST algorithm, but providing complete linkage between all
of the STs in the group.